Bio-Formats 5.3.0

Development plan

Oct 4, 2016

Bio-Formats 5.2: status

  • Aug 2016: 5.2.0 release (2016-06 model)
  • Sep-Oct 2016: 3 patch releases (bug fixes, IDR backporting)
  • Bio-Formats 5.3.0 proposal
    • Versioning
    • Architecture
    • API

Versioning: current status

  • Model/API breaking changes can be carried out in minor releases e.g. Bio-Formats 5.2.0
  • Consumers (e.g. OMERO 5.3.0-m2) need corresponding breaking changes
  • Release lifecycles: OMERO/Bio-Formats

Versioning: proposal

  • Move to semantic versioning
  • Major version X MUST be incremented if any backwards incompatible changes are introduced to the public API.
  • Minor version Y MUST be incremented if new, backwards compatible functionality is introduced to the public API.
  • Bio-Formats 5.3.0: API additions only
  • OMERO 5.3.0: seamless transition to Bio-Formats 5.x


  • Upcoming use cases
    • Glencoe Software: JPEG-XR library
    • Heterogenous metadata (MULTIMOT, Wellcome)
    • High-performance format containers

Integration: limitations

Monolithic block

Integration: proposal

Components re-architecture

Tiling API: status

  • Strong support for reading tiles
  • Need for greater transparency, documentation and samples in tiled writers
  • Few writers support complete tiling implementation (incl. TIFF)

Tiling API: proposal

  • API extension to improve usability of tiled Java writers
  • New methods in IFormatWriter to set/read the tile size
  • New options to enable/disable tiling by default
  • Expanded test coverage, documentation and samples

Options API: proposal

  • API to pass options using key/value pairs
  • Use cases
    • IDR: memoization
    • Tile vs non-tile writing
    • Reader-level options
  • Flexible, give more user control


  • 2 months (November 2016)
  • Milestone 1: Architecture/integration
  • Milestone 2: API additions
  • Maintain 5.2.x line for bug fixes?